gmx_qk

Good day and welcome to the gmx_qk!!. This is a Zenity, Python and gromacs dependent bash program. It is designed for beginners to the gromacs who would like to simulate the Protein-Ligand Complex. Gmx_qk is a fully automated program that works well with Gromacs versions 5.0 and 2021.4.

Informative and question widgets are supported by Zenity (GUI).

https://github.com/harry-maan.

About

Workflow

Installation gmx_qk

  1. Download the package from
  2. Open the terminal and run “bash configure.sh” gmx_qk will be appeared in the applications menu.
  3. Click on gmx_qk

Step 1: Launching gmx_qk in terminal

  1. Open the terminal and run “gmx_qk”

Step 2: Select gromacs

  1. Select executable gromacs usually gromacs installed in /usr/local/ or /opt

Step 2: Select Protein or Receptor file

  1. This is a zenity supported widget “Please select a receptor file (.pdb)
  2. Receptor file can be downloaded from https://www.rcsb.org/
  3. Make your receptor file clean using https://charmm-gui.org/ or whatever else you are familiar to the protein preparation tools.
  4. Remove all the hetero atoms i.e., ions, ligand, free water or solvent.

Step 3: Select a ligand file (.pdb)

  1. This is a zenity supported widget “Please select a ligand file (.pdb)
  2. ligand file can be downloaded from https://pubchem.ncbi.nlm.nih.gov/ as 3D .sdf or copy Canonical SMILES and paste in the http://zarbi.chem.yale.edu/ligpargen/
  3. Download the zipped file from ligpargen sever.
  4. Extract zip file which has name.pdb and name.itp(required for next step)

Step 4: Select a ligand parameter file (.itp)

  1. This is a zenity supported widget “Please select a ligand file (.itp)
  2. .itp file generated via http://zarbi.chem.yale.edu/ligpargen/ in the zipped file.(Downloaded in the last step)

Step 4: Select a task would you like to perform

  1. Select a task from drop down menu and click “ok”
  2. If topology chosen by the user: > It will generate the topology for a complex in the zipped file named “topology.tar.gz”. > It consists all the input files i.e., receptor.pdb, ligand.pdb, ligand.itp, conf.gro, topol.top and posre.itp.

  1. If Simulate the P-L complex chosen by the user: > It will ask for MD simulation parameters: > Enter the digits only as pico-seconds in first entry (Please be aware with your machine configuration it is directly related with time taken to complete the simulations ) > Enter the digits only as no. of steps required to minimize the energy of the system in second entry (5000 steps are looking fine) > Enter the name of file would you like assigned to the output file (Do not give a space in the file name) > Simulations will be started after
  1. Solvation of the complex system
  2. Addition of the counter ions (To equilibrate the system)

Step 6: Output file and its content

Step 7: Thankyou for using gmx_qk

Please feel free to contact me : https://github.com/harry-maan